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Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field
Changwon Yang1, Manho Lim1, Eunae Kim2
1Department of Chemistry and Institute of Functional Materials, Pusan National University , Busan 46241, South Korea.
Abstract:
We proposed a simple van der Waals backbone correction (O2' and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal Lorentz-Berthelot combination rule. As tested on four different tetranuceotides such as r(GACC), r(CCCC), r(AAAA), and r(CAAU), this new force field correctly captured each native fold as the largest population. For a RNA tetraloop (UUCG) tested, the stability of its native fold is substantially improved.
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